Reactome Plant to Cytoscape - possible?
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5.3 years ago
boczniak767 ▴ 870

Hi, are there pathway files (Reactome Plant) which can be loaded to cytoscape to recreate the shapes and arrangement of nodes and edges? Similarly as for animals with reactomefi app. I can recall seeing something like that some time ago but now I can't find it. I'm aware of existing biopax and sbgn files at the pathway subpage, but its not what I'm searching for.

Best Regards, Maciej

cytoscape network • 1.6k views
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How did you map your genes against Plant Reactome?

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I'm working on maize and Plant Reactome has maize IDs (version 4). So I don't have to map my genes.

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5.3 years ago
xanderpico ▴ 580

There is a Cytoscape app for Reactome: http://apps.cytoscape.org/apps/reactomefiplugin. I'm not sure if it supports Plant Reactome or not, but it is worth a try. Otherwise, as you already mentioned, Cytoscape can directly read BioPAX or SBML files, which you can download from Plant Reactome.

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Unfortunately the reactomefi doesn't support plants.

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